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Commit 13e8c6b4 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'feature-s/update_classification_for_fresh_install' into 'dev'

update classifications and configurations

See merge request !931
parents 38108d2f 3c6ed676
Pipeline #234643 failed with stages
in 45 seconds
...@@ -408,6 +408,10 @@ test_server_unit: ...@@ -408,6 +408,10 @@ test_server_unit:
artifacts: artifacts:
reports: reports:
junit: server/web2py/applications/vidjil/tests/test/TEST-*.xml junit: server/web2py/applications/vidjil/tests/test/TEST-*.xml
when: always
expire_in: 1 week
paths:
- server/web2py/ap‎plications/vidjil‎/tests/
only: only:
- /^feature-.*s.*\/.*$/ - /^feature-.*s.*\/.*$/
- /^hotfix-.*s.*\/.*$/ - /^hotfix-.*s.*\/.*$/
......
...@@ -622,24 +622,28 @@ def init_db_helper(db, auth, force=False, admin_email="plop@plop.com", admin_pas ...@@ -622,24 +622,28 @@ def init_db_helper(db, auth, force=False, admin_email="plop@plop.com", admin_pas
### Base config classification ### Base config classification
db.classification.insert( db.classification.insert(
name = 'Vidjil-algo', name = 'Human V(D)J recombinations',
info = 'Vidjil-algo' info = 'Analysis with vidjil-algo of human TR/IG recombinations'
) )
db.classification.insert( db.classification.insert(
name = 'Sub groups', name = 'Other recombinations',
info = 'Sub groups' info = 'Analysis with vidjil-algo of human non-V(D)J recombinations'
) )
db.classification.insert( db.classification.insert(
name = 'Other germlines', name = 'Analysis with/for other software',
info = 'Other germlines' info = 'Analysis that use other repertoire software or generate with vidjil-algo compatible output formats'
) )
db.classification.insert( db.classification.insert(
name = 'Other species', name = 'Other species',
info = 'Other species' info = 'Analysis with vidjil-algo of V(D)J recombinations for other species. Contact us at support@vidjil.org should you need other species.'
) )
db.classification.insert( db.classification.insert(
name = 'Experimentals', name = 'Experimental configs',
info = 'Experimentals' info = '"Experimental analyses, under development,may evolve without notice.'
)
db.classification.insert(
name = 'Old configs, do not use',
info = '"Old configurations. We do not recommend to use them. Should you need something, contact us at support@vidijl.org'
) )
...@@ -693,6 +697,22 @@ def init_db_helper(db, auth, force=False, admin_email="plop@plop.com", admin_pas ...@@ -693,6 +697,22 @@ def init_db_helper(db, auth, force=False, admin_email="plop@plop.com", admin_pas
info = 'IGH, Vh(Dh)Jh', info = 'IGH, Vh(Dh)Jh',
classification = 2 classification = 2
) )
db.config.insert(
name = 'Clonality',
program = 'vidjil',
command = '-c clones -3 -z 100 -r 1 -g germline/homo-sapiens.g -e 1 -2 -w 90 -y all --no-airr',
fuse_command = '-t 100 -d lenSeqAverage --overlaps',
info = 'incomplete germlines + larger window (90bp), thus 20bp more on each side. This configuration is advised for studies on IGH clonality',
classification = 1
)
db.config.insert(
name = 'Export all clones (AIRR)',
program = 'vidjil',
command = '-c clones -3 -y all -z all -g germline/homo-sapiens.g -e 1 -2 -d -w 50 -r 5 --no-vidjil',
fuse_command = '-t 100',
info = 'Export all clones in the tabular AIRR format. The results can not be browsed online. See http://www.vidjil.org/doc/vidjil-algo/#airr-tsv-output',
classification = 3
)
## permission ## permission
## system admin have admin/read/create rights on all patients, groups and configs ## system admin have admin/read/create rights on all patients, groups and configs
......
...@@ -64,4 +64,17 @@ class BrowserTest < MiniTest::Test ...@@ -64,4 +64,17 @@ class BrowserTest < MiniTest::Test
end end
end end
def teardown
#Save image if test fails
unless passed?
#Where to save the image and the file name
folder_path = File.expand_path(File.dirname(__FILE__))
folder_path.sub! '/functional', ''
screenshot_file = folder_path+"/screenshot_teardown_#{Time.now.strftime('%Y%m%d-%H%M%S')}.png"
#Save the image
$b.screenshot.save screenshot_file
end
end
end end
load 'browser_test.rb' load 'browser_test.rb'
class ServerTest < BrowserTest class ServerTest < BrowserTest
def self.test_order ## Comment to allow test to run in writing order; allow to debug error
:random # def self.test_order
end # :random
# end
end end
...@@ -360,7 +360,7 @@ class TestSample < ServerTest ...@@ -360,7 +360,7 @@ class TestSample < ServerTest
table = go_to_set_by_tag "#set_assoc_0" table = go_to_set_by_tag "#set_assoc_0"
config_list = $b.select_list(:id => "choose_config") config_list = $b.select_list(:id => "choose_config")
assert ( config_list.optgroup(:label => "Vidjil-algo").exist? ), "optgroup is present in configlist" assert ( config_list.optgroup(:label => "Human V(D)J recombinations").exist? ), "optgroup is present in configlist"
config_list.select("2") config_list.select("2")
Watir::Wait.until(timeout: 30) {$b.execute_script("return jQuery.active") == 0} Watir::Wait.until(timeout: 30) {$b.execute_script("return jQuery.active") == 0}
......
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